The non-coding RNA composition of the mitotic chromosome by 5'-tag sequencing

Nucleic Acids Res. 2016 Jun 2;44(10):4934-46. doi: 10.1093/nar/gkw195. Epub 2016 Mar 25.


Mitotic chromosomes are one of the most commonly recognized sub-cellular structures in eukaryotic cells. Yet basic information necessary to understand their structure and assembly, such as their composition, is still lacking. Recent proteomic studies have begun to fill this void, identifying hundreds of RNA-binding proteins bound to mitotic chromosomes. However, by contrast, there are only two RNA species (U3 snRNA and rRNA) that are known to be associated with the mitotic chromosome, suggesting that there are many mitotic chromosome-associated RNAs (mCARs) not yet identified. Here, using a targeted protocol based on 5'-tag sequencing to profile the mammalian mCAR population, we report the identification of 1279 mCARs, the majority of which are ncRNAs, including lncRNAs that exhibit greater conservation across 60 vertebrate species than the entire population of lncRNAs. There is also a significant enrichment of snoRNAs and specific SINE RNAs. Finally, ∼40% of the mCARs are presently unannotated, many of which are as abundant as the annotated mCARs, suggesting that there are also many novel ncRNAs in the mCARs. Overall, the mCARs identified here, together with the previous proteomic and genomic data, constitute the first comprehensive catalogue of the molecular composition of the eukaryotic mitotic chromosomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3T3 Cells
  • Animals
  • Chromosomes, Mammalian / chemistry*
  • High-Throughput Nucleotide Sequencing
  • Metaphase / genetics
  • Mice
  • Mitosis / genetics*
  • RNA, Untranslated / analysis*
  • RNA, Untranslated / chemistry
  • RNA, Untranslated / isolation & purification
  • Sequence Analysis, RNA
  • Sequence Tagged Sites


  • RNA, Untranslated